Predicting minimum energy structure of a peptide via a modified potential smoothing kernel
Leong, Wah June and Abu Hassan, Malik (2008) Predicting minimum energy structure of a peptide via a modified potential smoothing kernel. Malaysian Journal of Mathematical Sciences, 2 (2). pp. 29-39. ISSN 1823-8343; ESSN: 2289-750X
Official URL: http://einspem.upm.edu.my/journal/volume2.2.php
A global optimization approach is proposed for finding the global minimum energy configuration of a peptide. First, the original nonsmooth total potential energy function of a peptide, composed using the AMBER model, is transformed to a smoother function (shifted-impulsive transformation) via a procedure performed for each pair potential that constitute the total potential energy function. Then, the Potential Smoothing and Search (PSS) procedure is used to provide the global minimum. Based on this procedure global optimum solution is generated for a synthesis peptide named Compstatin.
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